User Tools

Site Tools


r-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
Next revisionBoth sides next revision
r-software [2021/01/25 12:39] aorthr-software [2022/05/18 07:41] aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 4.0 (4.0.3)+  * Version: 4.0 (4.0.5)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: December2020+  * Updated: May2021
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
 ===== Usage ===== ===== Usage =====
  
-See versions of R that are available:+See which versions are available:
 <code>$ module avail R</code> <code>$ module avail R</code>
  
Line 26: Line 26:
  
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://cran.r-project.org/src/base/R-4/R-4.0.3.tar.gz +$ wget https://cran.r-project.org/src/base/R-4/R-4.0.5.tar.gz 
-$ cd R-4.0.3+$ tar xf R-4.0.5.tar.gz 
 +$ cd R-4.0.5
 # install packages to enable capabilities in R # install packages to enable capabilities in R
 $ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64 $ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64
Line 37: Line 38:
 $ ./configure --enable-R-shlib --prefix=/export/apps/R/4.0 $ ./configure --enable-R-shlib --prefix=/export/apps/R/4.0
 $ make -j4 $ make -j4
 +$ sudo mv /export/apps/R/4.0.3
 $ sudo mkdir -p /export/apps/R/4.0 $ sudo mkdir -p /export/apps/R/4.0
 $ sudo chown aorth:aorth /export/apps/R/4.0 $ sudo chown aorth:aorth /export/apps/R/4.0
-$ make install</code>+$ make install 
 +$ sudo rm -rf /export/apps/R/4.0.3</code>
  
 Then install some common libraries used by our users because some of them are quite complicated, and installing them globally saves tens of thousands of header files and libraries being installed into user libraries anyways: Then install some common libraries used by our users because some of them are quite complicated, and installing them globally saves tens of thousands of header files and libraries being installed into user libraries anyways:
Line 50: Line 53:
 > install.packages("poppr", repos="https://cran.r-project.org") > install.packages("poppr", repos="https://cran.r-project.org")
 > install.packages("vcfR", repos="https://cran.r-project.org") > install.packages("vcfR", repos="https://cran.r-project.org")
 +> install.packages("devtools", repos="https://cran.r-project.org")
 +> library(devtools)
 +> install_github("HenrikBengtsson/TopDom")
 +> install_github("lucidif/HiCeekR", repos=BiocManager::repositories())
 > q() > q()
 $ sudo chown -R root:root /export/apps/R/4.0</code> $ sudo chown -R root:root /export/apps/R/4.0</code>
r-software.txt · Last modified: 2023/07/12 06:39 by aorth